St. Francis did not consider preaching the Gospel to save Muslim souls to be incompatible with the use of force to defend Christian lives
He respected the Pope's call for military action to protect Christian lives and property in the Middle East. Yet at the same time Francis attempted to convert Muslims to Christianity, and risked martyrdom himself in order to do so.
Documentation for the saint's support of the Fifth Crusade, upon which he embarked in 1219, comes from numerous sources. Pope Innocent III had initially laid the plans for this Crusade, but it was Pope Honorius III who launched it in 1217. Two years later, St. Francis along with a dozen followers, embarked on one of the galleys comprising the Crusader fleet, as it left Ancona, Italy. He disembarked in Syria to visit his friars of his Order in that area, and then resumed his journey on another Crusader vessel. He finally reached the city of Damietta in Egypt, a Muslim port city on the Nile under siege by the Crusader army. The main Muslim force, led by their king, Sultan al-Kamil, was encamped further up the river.
Risking martyrdom, during a temporary truce he crossed over to the camp of the Sultan's army. Francis and one other member of his Order (who probably was the interpreter), were captured by the sentries, beaten, and carried in chains to al-Kamil, after indicating that they wanted to speak to him. He explained to the Sultan that he was not an emissary sent by the Crusaders, but was sent by God to proclaim the gospel message of salvation taught by Jesus Christ. Impressed by the courage of Francis, the Sultan listened to him intently as the Faith was preached to him and his attendants, apparently over a number of days.
The saint did not directly attack the religion of Mohammed, but confined his discourse to expounding the truths of the Christian religion. He told the Sultan that he was concerned about his salvation, since if the Sultan refused to believe, God would not accept his soul. In addition he said that it was just that the Christians invade the land his followers inhabit, since they blaspheme the name of Christ and alienate everyone they can from His worship.
A foremost expert on Francis and the Fifth Crusade, Professor James Powell, wrote: "Francis of Assisi went to Damietta on a mission of peace. There can be no question about this. We should not however try to make him a pacifist or to label him as a critic of the crusade." Another leading crusade scholar, Christoph Maier, was even more explicit: "Francis thus accepted the crusade as both legitimate and ordained by God, and he was quite obviously not opposed to the use of violence when it came to the struggle between Christians and Muslims." Another historian noted that "unreserved support of the crusade had become normative in the Order."
Detailed references for the sources mentioned are available in my work, St. Francis of Assisi and the Conversion of the Muslims, published by TAN Books.